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Top Forums Shell Programming and Scripting Selectively deleting newlines with sed Post 303025726 by Xterra on Saturday 10th of November 2018 03:38:00 PM
Old 11-10-2018
Selectively deleting newlines with sed

I have a file that look like this:
Code:
>Muestra-1
agctgcgagctgcgaccc
gggttatata
ggaagagacacacacaccccc
>Muestra-2
agctgcg
agctgcgacccgggttatataggaagagac
acacacaccccc
>Muestra-3
agctgcgagctgcgaccc
gggttatata
ggaagagacacacacaccccc

I use the following sed script to remove newlines from lines not starting with >
Code:
sed ':a /^>/!N;s/\r\?\n\([^>]\)/\1/;ta'

I was trying to use b instead of t. So, this is what I did:
Code:
sed '/^>/!{:a;N;$!ba};s/\r\?\n//g'

but didnt get the desired result. Is there any way to use b in the second script to eliminate the newlines skipping those ones that start with >?
 

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SED(1)							      General Commands Manual							    SED(1)

NAME
sed - stream editor SYNOPSIS
sed [ -gln ] [ -e script ] [ -f sfile ] [ file ... ] DESCRIPTION
Sed copies the named files (standard input default) to the standard output, edited according to a script of commands. The -f option causes the script to be taken from file sfile; these options accumulate. If there is just one -e option and no -f's, the flag -e may be omitted. The -n option suppresses the default output; -g causes all substitutions to be global, as if suffixed g. The -l option causes sed to flush its output buffer after every newline. A script consists of editing commands, one per line, of the following form: [address [, address] ] function [argument ...] In normal operation sed cyclically copies a line of input into a pattern space (unless there is something left after a command), applies in sequence all commands whose addresses select that pattern space, and at the end of the script copies the pattern space to the standard out- put (except under -n) and deletes the pattern space. An address is either a decimal number that counts input lines cumulatively across files, a that addresses the last line of input, or a con- text address, /regular-expression/, in the style of regexp(7), with the added convention that matches a newline embedded in the pattern space. A command line with no addresses selects every pattern space. A command line with one address selects each pattern space that matches the address. A command line with two addresses selects the inclusive range from the first pattern space that matches the first address through the next pattern space that matches the second. (If the second address is a number less than or equal to the line number first selected, only one line is selected.) Thereafter the process is repeated, looking again for the first address. Editing commands can be applied to non-selected pattern spaces by use of the negation function (below). An argument denoted text consists of one or more lines, all but the last of which end with to hide the newline. Backslashes in text are treated like backslashes in the replacement string of an command, and may be used to protect initial blanks and tabs against the stripping that is done on every script line. An argument denoted rfile or wfile must terminate the command line and must be preceded by exactly one blank. Each wfile is created before processing begins. There can be at most 120 distinct wfile arguments. a text Append. Place text on the output before reading the next input line. b label Branch to the : command bearing the label. If label is empty, branch to the end of the script. c text Change. Delete the pattern space. With 0 or 1 address or at the end of a 2-address range, place text on the output. Start the next cycle. d Delete the pattern space. Start the next cycle. D Delete the initial segment of the pattern space through the first newline. Start the next cycle. g Replace the contents of the pattern space by the contents of the hold space. G Append the contents of the hold space to the pattern space. h Replace the contents of the hold space by the contents of the pattern space. H Append the contents of the pattern space to the hold space. i text Insert. Place text on the standard output. n Copy the pattern space to the standard output. Replace the pattern space with the next line of input. N Append the next line of input to the pattern space with an embedded newline. (The current line number changes.) p Print. Copy the pattern space to the standard output. P Copy the initial segment of the pattern space through the first newline to the standard output. q Quit. Branch to the end of the script. Do not start a new cycle. r rfile Read the contents of rfile. Place them on the output before reading the next input line. s/regular-expression/replacement/flags Substitute the replacement string for instances of the regular-expression in the pattern space. Any character may be used instead of For a fuller description see regexp(7). Flags is zero or more of g Global. Substitute for all non-overlapping instances of the regular expression rather than just the first one. p Print the pattern space if a replacement was made. w wfile Write. Append the pattern space to wfile if a replacement was made. t label Test. Branch to the command bearing the label if any substitutions have been made since the most recent reading of an input line or execution of a If label is empty, branch to the end of the script. w wfile Write. Append the pattern space to wfile. x Exchange the contents of the pattern and hold spaces. y/string1/string2/ Transform. Replace all occurrences of characters in string1 with the corresponding character in string2. The lengths of string1 and string2 must be equal. !function Don't. Apply the function (or group, if function is only to lines not selected by the address(es). : label This command does nothing; it bears a label for b and t commands to branch to. = Place the current line number on the standard output as a line. { Execute the following commands through a matching only when the pattern space is selected. An empty command is ignored. EXAMPLES
sed 10q file Print the first 10 lines of the file. sed '/^$/d' Delete empty lines from standard input. sed 's/UNIX/& system/g' Replace every instance of by sed 's/ *$// drop trailing blanks /^$/d drop empty lines s/ */ replace blanks by newlines /g /^$/d' chapter* Print the files chapter1, chapter2, etc. one word to a line. nroff -ms manuscript | sed ' ${ /^$/p if last line of file is empty, print it } //N if current line is empty, append next line /^ $/D' if two lines are empty, delete the first Delete all but one of each group of empty lines from a formatted manuscript. SOURCE
/src/cmd/sed.c SEE ALSO
ed(1), grep(1), awk(1), lex(1), sam(1), regexp(7) L. E. McMahon, `SED -- A Non-interactive Text Editor', Unix Research System Programmer's Manual, Volume 2. BUGS
If input is from a pipe, buffering may consume characters beyond a line on which a command is executed. SED(1)
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